--keep-dup: 保留重复。默认MACS(auto)会使用二项分布估计每个位置上是否存在重复(默认是1,也就是每个位置上出现一个read的概率最大)。如果你前期已经去重,那就使用all省了这一步. callpeak结果文件说明 callpeak会得到如下文件: NAME_peaks.xls: 以表格形式存放peak信息,虽然后缀是xls,但其实能用文本编辑器打开...
--keep-dup: 保留重复。默认MACS(auto)会使用二项分布估计每个位置上是否存在重复(默认是1,也就是每个位置上出现一个read的概率最大)。如果你前期已经去重,那就使用 all省了这一步. callpeak结果文件说明 callpeak会得到如下文件: NAME_peaks.xls: 以表格形式存放peak信息,虽然后缀是xls,但其实能用文本编辑器打...
Variousoptionstoindicate/controlinput,output,peakmodellingandpeakcallingmacs2callpeakusage:macs2callpeak[-h]-tTFILE[TFILE...][-c[CFILE[CFILE...]]][-f{AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE,BAMPE}][-gGSIZE][--keep-dupKEEPDUPLICATES][--buffer-sizeBUFFER_SIZE][--outdirOUTDI...
--keep-dup KEEPDUPLICATES It controls the MACS behavior towards duplicate tags at the exact same location -- the same coordination and the same strand. The 'auto' option makes MACS calculate the maximum tags at the exact same location based on binomal distribution using 1e-5 as pvalue cuto...
elegans (9e7) and dm for fruitfly (1.2e8), Default:hs -keep-dup KEEPDUPLICATES It controls the MACS behavior towards duplicate tags at the exact same location - the same coordination and the same strand. The auto option makes MACS calculate the maximum tags at the exact 16、 same ...
[--keep-dupKEEPDUPLICATES] [--buffer-sizeBUFFER_SIZE][--outdirOUTDIR][-nNAME] [-B][--verboseVERBOSE][--trackline][--SPMR] [-sTSIZE][--bwBW][-mMFOLDMFOLD][--fix-bimodal] [--nomodel][--shiftSHIFT][--extsizeEXTSIZE] [-qQVALUE][-pPVALUE][--to-large][--ratioRATIO] [--...
keep-dup KEEPDUPLICATES,-buffer-size BUFFER_SIZE,-outdir OUTDIR-n NAME,-B-verbose VERBOSE-trackline-SPMR,-s TSIZE-bw BW-m MFOLD MFOLD-fix-bimodal,-nomodel-shift SHIFT-extsize EXTSIZE,-q QVALUE-p PVALUE-to-large-ratio RATIO,-down-sample-seed SEED-nolambda,-slocal SMALLLOCAL-llocal...
[--keep-dup KEEPDUPLICATES] [--buffer-size BUFFER_SIZE] [--outdir OUTDIR] [-n NAME] [-B] [--verbose VERBOSE] [--trackline] [--SPMR] [-s TSIZE] [--bw BW] [-m MFOLD MFOLD] [--fix-bimodal] [--nomodel] [--shift SHIFT] [--extsize EXTSIZE] [-q QVALUE] [-p PVALUE...
keep-dup 1 --bdg --qvalue 0.05 # ARGUMENTS LIST: # name = MACS2 # format = BED # ChIP-seq file = ['/home/ogaard/gits/galaxy2/database/files/000/dataset_140.dat'] # control file = ['/home/ogaard/gits/galaxy2/database/files/000/dataset_116.dat'] # effective genome size =...
--keep-dup:该选项控制在完全相同的位置的重复tags的行为。“auto”选项使MACS基于使用1e-5作为pvalue截止的二项式分布计算在完全相同的位置的maximum tags;“all”选项保留每个标签。如果给定一个整数,最多这个数量的标签将被保留在同一个位置。注意,如果已经使用samtools或picard将reads标记为“PCR/Optical duplicate...